LECTURE 1 & 2 week one
LECTURE 1 & 2 week one BIOL 2460-001
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Lecture 1 Notes Tuesday September 1 2015 0954 NE Pay attention to bold words and highlighted words Why do we study microbiology 0 To understand microorganisms To know where are they found 0 To learn how to identify them 0 To learn their activities 0 To understand how they affect us 0 To learn how to control them For years scientists have believed that dust particles or minerals in clouds caused water droplets to coalesce into larger droplets and form rain snow or hail However recent research shows that bacteria are the predominant particles that induce the formation of precipitation After a hailstorm hit the Montana State University campus in Bozeman Montana Alexander Michaud and his collaborators gathered hailstones larger than 5 cm in diameter separated them into four layers and analyzed them as they melted They were surprised to find that Pseudomonas syringae a species of bacteria that is commonly implicated in infections of plants and as the cause of postharvest rots grew from the water in the hailstones Michaud explains that bacteria found in the embryo the first part of the hailstone to develop initiate the growth of a hailstone quotIn order for precipitation to occur a nucleating particle must be present to allow for aggregation of water molecules he states quotThere is growing evidence that these nuclei can be bacteria or other biological particles 0 Why do you think that climate scientists never realized that microbes actually caused nucleation of water droplets in clouds How does P syringae make it rain at warm temperatures Brent Christner a scientist who worked with Michaud has studied snow samples from around the world Christner has found that bacteria are the most common warm temperature rain and snow nucleators P syringae isn t the only biological nucleator of ice other bacteria fungi diatoms and algae can serve as nucleators as well Water vapor in clouds freeze at temperatures below 35 C but nucleators such as P syringae can cause this to happen at much warmer temperatures The bacteria possess a protein structure that provides a framework where free floating water molecules can attach When the water vapor clings to the bacteria and to other water molecules it can freeze and fall back to the earth Until this discovery atmospheric scientists never realized the impact that biological nucleators had on the formation of rain snow and hail It turns out that bacteria have been making it rain all along J Craig Venter a genomic researcher 0 Using molecular biology techniques first developed for the Human Genome Project Venter hoped to classify the new life forms by identifying novel genes without having to coax organisms to grow in the lab J Craig Venter s initial efforts led to the discovery of 12 million new genes and 1800 new species 0 He heads an organization called the Institute for Biological Energy Alternatives 0 One of the institute s goals is to create synthetic organisms tailor made for a specific purpose such as synthesizing chemicals degrading waste products or producing energy 0 It stands to reason that Venter s discovery of new species will increase the potential for even more useful products both naturally occurring and man made What is Microbiology Microbiology is the specialized area of biology that deals with the study of organisms that require magnification to be observed gt1mm less than 2 micrometers um one millionth of a meter Microbiology is one of the largest and most complex of the biological sciences because it includes many diverse biological disciplines Employs techniques Sterilization and the use of culture media necessary for isolation and growth of microorganisms Microscopic small o The six types of microorganisms The Bacteria monera Prokaryotes also include the Archaea and have no nucleus A lot of diversity within this group of organisms Single celled prokaryotes Reproduce asexually Specific shapesmorphology seven basic shapes Most are smaller than the eukaryotes Decomposers Most have rigid cell walls accountable for the shape of the organism Peptidoglycan contained within the cell wall of the bacteria identifying whether a bacteria is gram positive or gram negative Not found in the Archea or the Eucarya Fungh Eukaryotes have a nucleus Differ from plants obtain food from other organisms Differ from animals have a cell wall Includes mold and yeast Mold Examples cottony growths on cheese bread and jams Penicillium chrysogenum mold that produces penicillium Yeast Useful yeast Saccharomyces cerevisiae causes bread to rise and produces alcohol from sugar Problematic yeast Candida albicans yeast that causes most cases of yeast infections in women Algae Eukaryotes Photosynthetic organisms They make their own food from carbon dioxide and water using energy from the sunlight Contain single celled and multi cellular members contain a green pigment chlorophyll which absorb light which algae use a source of energy Characterized on the basis of their pigmentation Found near surface of either salt or fresh water 0 Cells walls are rigid but do not contain peptidoglycan Protozoa Eukaryotes singled celled similar to animals in their nutritional needs and cellular structure Protozoa is Greek for quotfirst animals Typically live free in water but some live inside animals where they can cause disease Viruses Not considered cells Neither prokaryotic nor eukaryotic Helminth Greek word means worm Collectively tapeworms flukes and roundworms Included among the microorganisms because of their infective abilities and the microscope is necessary to identify theirs eggs and larvae Microorganisms or Microbes Oldest organisms evolved over 35 38 billion years ago MicrobesWhere are they Ubiquitous means EVERYWHERE Microbiology A Sampler A Medical Microbiology This branch deals with microbes that cause diseases in humans and animals Researchers examine factors that make the microbes virulent and mechanisms for inhibiting them B Public Health Microbiology and Epidemiology These branches monitor and control the spread of diseases in communities C Immunology This branch studies the complex web of protective substances and cells produced in response to infection It includes such diverse areas as vaccination blood testing and allergy D Industrial Microbiology This branch safeguards our food and water and also includes biotechnology the use of microbial metabolism to arrive at a desired product ranging from bread making to gene therapy Microbes can be used to create large quantities of substances such as amino acids beer drugs enzymes and vitamins E Agricultural Microbiology This branch is concerned with the relationships between microbes and domesticated plants and animals Plant specialists focus on plant diseases soil fertility and nutritional interactions Animal specialists work with infectious diseases and other associations animals have with microorganisms F Environmental Microbiology These microbiologists study the effect of microbes on the earth s diverse habitats Whether the microbes are in freshwater or saltwater topsoil or the earth s crust they have profound effects on our planet Subdisciplines of environmental microbiology are 0 Aquatic microbiology the study of microbes in the earth s surface water 0 Soil microbiology the study of microbes in terrestrial parts of the planet 0 Geomicrobiology the study of microbes in the earth s crust 0 Astrobiology also known as exobiology the search forstudy of microbial and other life in places off of our planet What role do microorganisms play in our everyday life Involved in the flow of energy and food earth s ecosystem Photosynthesis Microorganisms MOs were photosynthesizing long before plants Responsible for changing the atmosphere of the earth from one without oxygen to one with oxygen Photosynthetic MOs 50 of earth s photosynthesis the majority of oxygen in atmosphere Plants Depend on microbes to help obtain nitrogen they need for survival Animals Cows and Sheep Need microbes in order to digest cellulose in their plant based diets Decomposition Breakdown of dead matter and wastes into simple compounds that can be directed back into the natural cycles of living things Nutrient recycling Keep the earth s balance Human Use of MOs Yeast Fungus causes bread to rise and ferment sugar into alcohol winebeer Ancient moldy bread apply to wounds development of vaccines and antibiotics Biotechnology humans use mos products industrial setting Genetic engineering areas of biotechnology that manipulates the genetics of microbes for creating new products and genetically modified organisms GMOs o Bacteria and fungi were among the first to be genetically altered o Microbes can be engineered to synthesize drugs hormones and enzymes Ecosystems Rely on microbes to enrich soil degrade wastes and support life Bioremediation This process involves the introduction of microbes into the environment to restore stability or to clean up toxic pollutants Microbes have a surprising capacity to break down chemicals that would be harmful to other organisms This includes even man made chemicals that scientists have developed and for which there are no natural counterparts Agencies and companies have developed microbes to handle oil spills and detoxify sites contaminated with heavy metals pesticides and other chemical wastes The solid waste disposal industry is interested in developing methods for degrading the tons of garbage in landfills especially human made plastics and paper products One form of bioremediation that has been in use for some time is the treatment of water and sewage Infectious Diseases and Human Condition Despite all of the benefits they provide they also contribute significantly to human misery as Pathogens c any agent usually a virus bacterium fungus protozoan or helminth that causes disease Disease causing microorganisms Disease infections diet genetics and aging Infection Pathogenic microbes penetrate tissue multiply damagedisrupt tissues and organs 0 Infectious Disease The state of damage or toxicity in the body caused by an infectious agent Lecture 2 Notes Tuesday September 1 2015 1039 NE Pay attention to bold words and highlighted words Historical Perspective of nursing microbiology No knowledge of disease or any of the medical knowledge of today it was the very act of caring for an individual that was the essence of their practice Slaves As civilization progressed through thousands of years new ideas and social constructs began to have an impact on nursing While some nurses were still skilled women with authority either in the family or employed by the wealthy most had become servants Physician A male who had specialized skills different from a nurse Nurse Most all societies were male dominated nurses were subservient to doctors The nurse s role had regressed to that of an assistant caregiver Religion Under the umbrella of religion because of perceived causes of illnesses diseases was viewed as an invasive demon sin or punishment from the gods Cures were scaring a demon out drilling holes in head to provide exit points for bad influences prayer rituals and even human sacrifices Middle Ages and Renaissance Medicine through scientific endeavor moved away from mysticism Nursing had moved from the slave quarters of wealthy families to the nunnery as well as few schools 16005 c The spiritual leadership of St Vincent de Paul had led to an enrichment of nursing He recognized that nursing could be a social force helping not only the ill but also the poor hungry sad and lonely He saw the need for and created a program for nursing education helping to start the Dames de Charit This was an early nursing group which later gave rise to the secular Sisters of Charity in 1633 Both were led by women and serve as the earliest examples of quotnursing schools Women of faith would put their hearts and souls into caring for the ill to answer a higher power It was here that the usage of sister becomes synonymous with nurse Florence Nightingale Florence was given social and educational opportunities not afforded to most Victorian era women She combined her intelligence and sense of humanity and began nursing in 1845 Always looking for new techniques or insights Nightingale s career took off in 1851 when she received four months39 training in Germany as a Deaconess of Kaiserswerth Hospital In England she was becoming well known for her skills as well as her push for healthcare reform By 1853 she had a post as superintendent at the Institute for the Care of Sick Gentlewomen in London In 1854 she and 40 nurses picked by her went to assist the military hospitals in Scutari during the Crimean war This was in response to public outcry at the high mortality rates being reported from frontline reporters contrary to official military releases Within two months of her arrival mortality rates in the barracks dropped from 42 to 2 o This was mostly due to her practice of rigorous sanitation and infection control Florence would use her social influence to change the face of nursing Known for introducing cleanliness and other antiseptic techniques into nursing History of Microbiology The Early years of microbiology brought the first observation of microbial life The Microscope the 3K Dutch spectacle maker Zacharias Janssen one of several who discovered that if two convex lenses were put together small objects would appear larger Around 1600 an instrument combined two lenses in a tube to increase magnification of an object the compound microscope Instrument was further developed as the 17th century arrived 1625 the term microscopio or microscope was actually referred to the invention Robert Hooke The Inspirational Father of Modern Science in England and the 39Father of English Microscopy39 Considered to have one of the most inventive and ingenious minds in the history of science First to take advantage of the magnification abilities of the compound microscope He wrote 39The Micrographia 166539 the first book describing observations made through a microscope including the first microorganism a common bread mold First microorganism described in this book is a common bread mold Observations with the microscope that had a magnification of 25X He used the word cella 200 years before the theory of the cell was fully developed and the word became known as cell The existence of microorganisms and their relationship to disease was suspected long before they could actually be seen but real physical evidence was not available until the invention of the microscope Antonie van Leeuwenhoek He was not the founder of the microscope was but was credited with the most careful and exacting observations of microbes with the single lens microscope He came from a family of tradesmen had no fortune received no higher education or university degrees and knew no languages other than his native Dutch He was a Dutch linen merchant and selfmade microbiologist Grinded glass lenses to see with clarity the thread in his fabrics Scraped the plaque from his teeth and from the teeth of several volunteers who had never cleaned their teeth in their lives Discovered microorganisms which he called quotanimalculesquot Father of bacteriology and protozoology Leeuwenhoek s microscopes were able to achieve 50300X magnification which enabled him to visualize a variety of bacteria and protozoa He communicated his findings to the Royal Society of London but kept his techniques for grinding lenses and making observations a secret Consequently his contemporaries had a very difficult time repeating his results He was recognized as a scientist of great merit The Golden Age of Microbiology Spontaneous generation shaped the science of microbiology It refers to the ancient belief that living organisms could arise spontaneously from nonliving matter The Greek philosopher Aristotle believed insects and other small animals had to arise from spontaneous generation because he was unable to observe organs including reproductive organs Flemish physician Jan Baptista van Helmont suggested that mice could spontaneously generate from decaying wheat bran and dirty shirts Others had witnessed decomposing wheat grains that generated worm like maggots Leeuwenhoek suggested that maggots did not arise from wheat grains but rather tiny eggs laid in the grain that he could see with his microscope Therefore requiring investigation and experimentation Spontaneous Generation had been accepted without any real proof ABIOGENESIS VS BIOGENESIS Abiogenesis Spontaneous generation Biogenesis Living things only arise from other living things The Decaying Meat Experiment Francesco Redi This belief prevailed until 1688 when Francesco Redi an Italian physician attempted to address the question of Spontaneous Generation experimentally He made careful observations of fly eggs and maggots by placing decaying meat in a jar Jar 1 The jar was left open maggots developed and flies were observed laying eggs on the meat in the openjan Jar 2 The jar was covered with fine gauze maggots appeared on the fine gauze and flies were observed laying eggs on the gauze These eggs produced maggots Jar 3 The jar was covered and sealed no maggots developed MEAT did not spontaneouslv generate maggots as previously believed Concluded spontaneous generation was not occurring Redi39s experiment did not settle the controversy of Spontaneous generation It was when the French Academy of Sciences sponsored a contest for the best experiment to prove or disprove spontaneous generation did the controversy settle Louis Pasteur the 39Father of Microbiology39 took on this challenge with the Swan Neck Flasks Experiment Swan Neck Flasks Experiment First he made flasks with bent 39swan39 necks This allowed air to enter but prevented the introduction of dust and microbes into the flask He filled the bottom of the flask with some broth microbes and boiled it long enough to kill anything inside the flask Nothing grew in the broth the broth was sterile Pasteur concluded that the contaminating particles in the air were trapped on the walls necks of the curved irregular flasks Finally Pasteur broke the neck of the flask and growth occurred 18 months later he reported that his swan necked flasks remained free of microbes Additional Roles that lead to Pasteur s role as the Father of Microbiology Invented pasteurization Completed some of the first studies showing human diseases could arise from infection Pasteur s discovery that bacteria are responsible for spoiling wine led naturally to his hypothesis in 1857 that microbes were responsible for disease This idea came to be known as the germ theory of disease Scientific Method Approach taken by scientific to explain a certain natural phenomenon The development of the experimental system that answered questions objectively The Scientific Method Hypothesis Predictions Testing Conclusion Theory Introduction of the Development of Medical Microbioloav In 1843 an American physician Oliver Wendall Holmes published a paper on Puerperal PURE PER AL sepsis which afflicted mothers during childbirth Holmes reported that it was much safer to deliver a baby at home than in a hospital where physician handling contribute to the disease Ignaz Semmelweis 18181865 A Hungarian physician on the obstetric ward of a teaching hospital in Vienna In 1848 noticed women giving birth in the wing where medical students were trained died from puerperal fever 20 X higher than the mortality rates of either women attended by midwives in adjoining wing or women who gave birth at home Semmelweis hypothesized that medical students and residents frequently handled cadavers in the morgue before coming to the maternity ward and carried quotcadaver particles were carried from their autopsy studies into the delivery room and these particles resulted in puerperal fever infections Puerperal fever Fever that lasts for more than 24 hours within the first 10 days after a woman has had a baby Puerperal fever is due to an infection most often of the placental site within the uterus If the infection involves the bloodstream it constitutes puerperal sepsis Semmelweis began requiring medical students to wash their hands with chlorinated lime water and mortality within the next year decreased from 183 to 13 Despite his success he was ridiculed for insisting that physicians wash their hands before working with pregnant women He was forced to leave the hospital by the director and returned to his native country Hungary where his techniques continued to produce higher patient survival rates Joseph Lister Impressed with Pasteur s studies on the involvement of microorganisms in fermentation Holmes and Semmelweis research in 1867 Joseph Lister an English surgeon modified and advanced the idea of antisepsis in health care settings He was considered the father of antiseptic surgery The first to introduce to aseptic techniques reducing microbes in a medical setting and preventing wound infections Developed a system of antiseptic surgery designed to prevent microorganisms from entering the wounds Demonstrated that boiling instruments heat sterilized and applying carbolic acid to dressings that covered wounds dramatically reduce the incidence of disease following surgery Phenol was used on surgical dressing and at time sprayed over the surgical area This approach transformed surgery Initially met with resistance but when he showed that this technique reduced deaths among his patients by two thirds his method was accepted as common practice He indicated Semmelweis Operation using Lister39s carbolic spray was invented in 1869 In 1870 Lister39s antiseptic methods were used by Germany during the Franco Prussian war saving many Prussian soldier39s lives In Germany by 1878 Robert Koch was demonstrating the usefulness of steam for sterilizing surgical instruments and dressings Robert Koch Koch a country German doctor began a race with Pasteur to discover the cause of anthrax Robert Koch demonstrated the first direct role of a bacterium in disease In 1872 1875 Koch began his work on the disease called anthrax which is a devastating disease that affects cattle often wiping out entire herds Anthrax is a common disease but can also be transmitted to humans In most common form of the disease B anthracis enters the body through skin abrasions Gets into the bloodstream Causes septicemia and death Toxins produce ulceration of the skin Koch established that a specific bacterium Bacillus anthracis was the cause of the disease in mammals Clearly linked a microscopic organism with a specific disease n 1880s he identified the bacterium that causes tuberculosis Mycobacterium tuberculosis and developed a method of staining the organism and disproved that it was inherited He also guided the research that led to the isolation of Vibrio cholerae found in feces contaminated water from a person infected with cholera and can also be found in aquatic sources such as brackish rivers and coastal water Other source is shellfish eaten raw and can most likely be isolated from fecal specimens In 1882 Paul Ehrlich published his method of staining the tubercle bacillus that Koch had discovered and this method was the basis of the subsequent modifications introduced by Ziehl and Neelson which are still used today From it was also derived the Gram method of staining bacteria so much used by modern bacteriologists Other Contributions of Koch and His Associates Koch s proof that Bacillus anthracis caused anthrax was independently confirmed by Pasteur and his coworkers They discovered that after burial of dead animals anthrax spores survived and were brought to the surface by earthworms Healthy animals then ingested the spores and became ill Koch also developed the media that was suitable for growing bacteria isolated from the human body many of which are still in use today Koch also invented nutrient broth and nutrient agar Koch developed and reported the simple stain technique in 1877 o The use of steam to sterilize growth media Aseptic laboratory techniques such as transferring bacteria between media using a platinum wire that had been heat sterilized in a flame Elucidation of bacteria as distinct species KOCH S POSTU LATES In 1881 Koch proposed 4 postulates that could be used to prove whether or not an infectious agent is the cause of a disease These postulates verified established whether organism was pathogenic and which disease it caused It is the scientific method of establishing the Germ Theory of Disease The causative agent must be present in every case of the disease and absent in healthy animals The agent of disease can be isolated from the diseased animal and can be grown in pure culture A population of one organism Ill The disease can be reproduced by inoculating a portion of the pure culture into healthy animals IV The agent of disease can be re isolated from the infected animal Nomenclature Binomial System Nomenclature a two word naming system c The first word is the genus and is always capitalized Second word is the species name and is not capitalized Both words are italicized Example Escherichia coli E coli Many bacteria are named after the person who first isolated and described it ie Theodor Escherich Species name comes from the location where the organism was found the colon The science of classifying living beings is taxonomy 0 It originated more than 250 years ago when Carl von Linn also known as Linnaeus 1701 1778 a Swedish botanist laid down the basic rules for classification and established taxonomic categories or taxa singular taxon The primary concerns of modern taxonomy are still naming classifying and identifying These three areas are interrelated and play a vital role in keeping a dynamic inventory of the extensive array of living and extinct beings In general Nomenclature is the assignment of scientific names to the various taxonomic categories and individual organisms Classification attempts the orderly arrangement of organisms into a hierarchy of taxa Identification is the process of discovering and recording the traits or organisms so that they may be recognized or named and placed in an overall taxonomic scheme The method of assigning a scientific or specific name is called the binomial two name system of nomenclature The scientific name is always a combination of the generic genus name followed by the species name 0 The generic part of the scientific name is capitalized and the species part begins with a lowercase letter 0 Both should be italicized or underlined if using handwriting as follows The two part name of an organism is sometimes abbreviated to save space as in S aureus but only if the genus name has already been stated 0 The source for nomenclature is usually Latin or Greek o If other languages such as English or French are used the endings of these words are revised to have Latin endings The inspiration for names is extremely varied and often rather imaginative Some species have been named in honor of a microbiologist who originally discover them